Sequences diagnostic for shrimp pathogens

Abstract

Primers have been isolated that are diagnostic for the detection of the infectious hypodermal and hematopoietic necorsis virus (IHHNV). The primers are based on a new portion of the IHHNV genome and may be used in primer directed amplification or nucleic acid hybridization assay methods.

1. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO: 1 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:1, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       2. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:2 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:2, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       3. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:3 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:3, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       4. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:4 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:4, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       5. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:5 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:5, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       6. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:6 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:6, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       7. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:7 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:7, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       8. An isolated IHHNV diagnostic primer sequence as set forth in SEQ ID NO:8 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO:8, wherein the primer sequence corresponds to a portion of the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       9. A pair of two different IHHNV diagnostic primer sequences of any of SEQ ID NOs:1-8 wherein the pair is capable of priming a nucleic acid amplification reaction that amplifies a region of nucleic acid within the IHHNV genome which is diagnostic for the presence of IHHNV. 
     
     
       10. A pair of two different IHHNV diagnostic primer sequences according to  claim 9  wherein the pair is selected from the group consisting of SEQ ID NOs: 1 and 2, SEQ ID NOs:3 and 4, SEQ ID NOs:5 and 6, SEQ ID NOs:7 and 8, and SEQ ID NOs:1 and 4. 
     
     
       11. A kit for the detection of IHHNV comprising at least one pair of IHHNV diagnostic primer sequences of  claim 9 , wherein said kit is diagnostic for the presence of IHHNV. 
     
     
       12. A kit for the detection of IHHNV according to  claim 10  wherein the kit further comprises at least one reagent selected from the group consisting of a thermostable polymerase, a mixture of four different deoxynucleotide triphosphates, a nucleic acid-binding fluorescent molecule, at least one pair of internal sample control primers, at least one internal template control and at least one pair of internal template control primers, and a probe comprising a complementary sequence to a portion of at least one region of nucleic acid within the IHHNV genome which is capable of being amplified with the at least one pair of IHHNV diagnostic primer sequences. 
     
     
       13. A method for detecting the presence of IHHNV in a sample comprising:
 (i) providing DNA from a sample suspected of containing the IHHNV; and 
 (ii) probing the DNA with a probe derived from the isolated IHHNV diagnostic primer sequence of any of  claims 1 - 8  under suitable hybridization conditions; 
 wherein the identification of a hybridizable nucleic acid fragment confirms the presence of IHHNV. 
 
     
     
       14. A method for detecting the presence of IHHNV in a sample according to  claim 13  wherein the probe derived from the isolated IHHNV diagnostic primer sequence is selected from the group consisting of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7 8, 9, 10, 11, 12, and the complete complimentary sequences thereof. 
     
     
       15. A method according to  claim 13  wherein the probe contains a replication inhibiting moiety at the 3′ end. 
     
     
       16. A method according to  claim 15  wherein the replication inhibiting moiety is selected from the group consisting of dideoxynucleotides, 3′ deoxynucleotides, a sequence of mismatched nucleosides or nucleotides, 3′ phosphate groups and chemical agents. 
     
     
       17. A method according to  claim 16  where in the 3′ deoxynucleotide is cordycepin. 
     
     
       18. A method for detecting the presence of IHHNV in a sample comprising:
 (i) providing DNA from a sample suspected of containing IHHNV; and 
 (ii) amplifying the DNA with at least one pair of IHHNV diagnostic primer sequences of  claim 9  such that amplification products are generated; 
 wherein the presence of amplification products confirms the presence of IHHNV. 
 
     
     
       19. A method for detecting the presence of IHHNV in a sample according to  claim 18  wherein the amplifying of (ii) is done using the polymerase chain reaction. 
     
     
       20. A method for detecting the presence of IHHNV in a sample according to  claim 18  wherein the amplifying of (ii) is done in the presence of a nucleic acid-binding fluorescent agent or a fluorescently labeled probe and the presence of amplification products is confirmed using fluorescence detection. 
     
     
       21. A method according to  claim 20  wherein the fluorescently labeled probe is selected from the group consisting of SEQ ID NO:17 and SEQ ID NO:18. 
     
     
       22. A method according to  claim 18  wherein at least one pair of internal sample control primers is included in the amplifying of (ii) to produce an internal sample control product. 
     
     
       23. A method according to  claim 22  wherein the at least one pair of internal sample control primers is selected from the group consisting of SEQ ID NOs:13,14 and SEQ ID NOs:15,16. 
     
     
       24. A method according to  claim 18  wherein at least one pair of internal template control primers and at least one internal template control are included in the amplifying of (ii) to produce an internal template control product. 
     
     
       25. A method for quantifying the amount of IHHNV in a sample comprising:
 (i) providing DNA from a sample suspected of containing IHHNV; 
 (ii) amplifying the DNA with at least one pair of IHHNV diagnostic primer sequences of  claim 9  by thermal cycling between at least a denaturing temperature and an extension temperature in the presence of a nucleic acid-binding fluorescent agent or a fluorescently labeled probe; 
 (iii) measuring the amount of fluorescence generated by the nucleic acid-binding fluorescent agent or the fluorescently labeled probe during the thermal cycling; 
 (iv) determining a cycle threshold number at which the amount of fluorescence generated by the nucleic acid-binding fluorescent agent or the fluorescently labeled probe reaches a fixed threshold value above a baseline value; and 
 (v) calculating the amount of IHHNV in the sample by comparing the cycle threshold number determined for the IHHNV in the sample with a standard curve of the cycle threshold number versus the logarithm of template concentration determined using standard solutions of known concentration. 
 
     
     
       26. A method according to  claim 25  where in the fluorescently labeled probe is selected from the group consisting of SEQ ID NO:17 and SEQ ID NO:18. 
     
     
       27. A method according to any of  claims 13 ,  18 , or  25  wherein the method further comprises the steps of:
 a) treating an environment from which the sample was obtained with a chemical treatment to kill or control the IHHNV; and 
 b) repeating the steps of the method of  claims 13 ,  18 , or  25  on another sample taken from the environment in order to assess IHHNV inactivation by the chemical treatment. 
 
     
     
       28. A method according to any of  claims 13 ,  18 , or  25  wherein the method further comprises the step of: treating an environment from which the sample was obtained with a chemical treatment to kill or control the IHHNV in order to improve the health and grow-out of shrimp.